SMTL ID : 1uvr.1

Structure of human PDK1 kinase domain in complex with BIM-8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.255, P.265, A.268, H.269, P.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.265 GOL.2: 7 residues within 4Å: Chain A: S.24, K.41, Y.56, V.57, E.60, G.155 Ligands: SO4.12 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:K.41, A:E.60 GOL.3: 4 residues within 4Å: Chain A: R.5, K.6, F.77, T.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.61, A:T.78 GOL.4: 5 residues within 4Å: Chain A: L.227, Y.229, D.230, F.231, R.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.227 GOL.5: 8 residues within 4Å: Chain A: R.36, E.37, Y.38, Y.76, S.90, Y.91 Ligands: SO4.10, SO4.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.91 GOL.6: 7 residues within 4Å: Chain A: H.69, S.121, W.277, E.278, N.279, L.280, H.281 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.121, A:L.280, A:H.281, A:H.281 Water bridges: A:H.69, A:E.124 GOL.7: 3 residues within 4Å: Chain A: F.12, K.13, F.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.12, A:F.14 GOL.8: 7 residues within 4Å: Chain A: G.19, E.20, G.21, S.24, V.26 Ligands: SO4.12, BI8.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:K.41

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain A: K.6, R.61, T.78, F.79, Q.80 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.80 Salt bridges: A:K.6, A:R.61 SO4.10: 4 residues within 4Å: Chain A: Y.76, S.90, Q.150 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.76, A:S.90, A:Q.150 SO4.11: 2 residues within 4Å: Chain A: R.36 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.36 SO4.12: 6 residues within 4Å: Chain A: G.21, S.22, F.23, S.24 Ligands: GOL.2, GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.22, A:F.23, A:S.24 Water bridges: A:K.41, A:K.41 Salt bridges: A:K.41

1 x BI8: 3-[1-(3-AMINOPROPYL)-1H-INDOL-3-YL]-4-(1-METHYL-1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE(Non-covalent)

BI8.13: 18 residues within 4Å: Chain A: L.18, G.19, A.39, K.41, E.60, V.73, L.89, S.90, Y.91, A.92, G.95, E.96, E.139, N.140, L.142, T.152, D.153 Ligands: GOL.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.18, A:K.41, A:L.89, A:L.142, A:T.152, A:D.153 Hydrogen bonds: A:S.90, A:A.92, A:E.139, A:E.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komander, D. et al., Interactions of Ly333531 and Other Bisindolyl Maleimide Inhibitors with Pdk1. Structure (2004)

Release Date

2004-03-04

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1

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